Dear all,
my system consists of one big receptor and several ligand molecules.
Before MMPBSA analysis
I would like to create new trajectory where is my receptor, ligand
molecules and several
(10 in this testing case) H2O molecules which are close to ligand
molecules bound to the receptor surface
but also close to surface groups of my receptor.
I tried to achieve this by performing "closestwater" command in two
consequent steps (using AmberTools 1.4).
A) To find the closest 50 water molecules to my ligand molecules (:ANS).
B) To choose from this 50 water molecules the closest 10 to surface
groups of my receptor (:G4A,0GA)
Unfortunately only step A) was successful. The final system obtained in
step B)
is not the one I expected as some far (from receptor) water molecules were
retained
and on the other hand some H2O molecules close to receptor surface were
deleted.
Here are 2 pictures where is shown situation after step A) and after step
B).
(receptor surface groups are in green, ligands in yellow and water is in
sphere representation)
http://physics.ujep.cz/~mmaly/AMBER/
Below is my procedure more in detail (with relevant commands used).
I would be grateful for any suggestions which could help me to get
expected results.
Thanks a lot in advance !
Best wishes,
Marek
#1
Just to save last (400th) frame from the original trajectory with
only 50 closest water molecules to my ligand molecules (:ANS)
---------------------------------------------------------------------------------
trajin prod_BASE_NAME_REIMAGED.mdcrd 400 400 1
trajout prod_BASE_NAME_REIMAGED_OUT1.mdcrd netcdf
trajout prod_BASE_NAME_REIMAGED_OUT1.pdb pdb
strip :Na+
solvent byres :WAT
closestwater 50 :ANS first noimage
--------------------------------------------------------------------------------
#2
The same as #1 just with output format PDB to create new PRMTOP file
#3
To retain only 10 closest H2O molecules (from that previously chosen 50)
to the surface groups (:G4A,0GA) of my
receptor and save as PDB file.
-----------------------------------------------------------
trajin prod_BASE_NAME_REIMAGED_OUT1.mdcrd 1 1 1
trajout prod_BASE_NAME_REIMAGED_OUT.pdb pdb
solvent byres :WAT
closestwater 10 :G4A,0GA first noimage
---------------------------------------------------------------
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Mon May 09 2011 - 13:30:03 PDT
